ANC secretary general Ace Magashule says it was Zizi Kodwa and Pule Mabe who each requested that they not fulfill their full responsibilities while they face separate claims of sexual violence.
On Tuesday morning, two national working committee (NWC) members told News24 that a decision had been taken for the pair to "step aside" from their roles as official spokespersons for the party.
Magashule said the party respected their decisions to step aside.
He said the NWC had noted the allegations and viewed them as serious.
He added the party stood against gender violence and would not tolerate violence against women perpetrated by members of the party.
Magashule said they were not judges and wanted to afford everybody involved the opportunity to respond.
On Saturday, ANC deputy secretary general Jessie Duarte confirmed that a woman had sent a rape complaint against a high-ranking official to the office of the secretary general.
Duarte said the party had advised the woman to approach the police with her complaint.
"The advice we've given the complainant is that she needs to go to the criminal justice system with her complaint," Duarte said.
On Sunday, Kodwa denied the claims against him, saying they were "replete with false accusations".
He described it as a "dirty tricks campaign" aimed at "political blackmail and manipulation".
In December, Mabe's former personal assistant, Kgoerano Kekana, accused him of sexual harassment.
The matter was heard by a grievance panel and Mabe was subsequently cleared of all charges.
Last week, Kekana released a statement saying she had rejected the panel's findings.
She said she would explore other avenues, including approaching the police and the CCMA, to have the matter dealt with effectively.
While the ANC said Mabe would return to work after he was cleared, both he and the party now say he is actually on extended leave and has requested to continue working for the party from home.